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Hirzler H, Trimby E, Gerritsma R, Safavi-Naini A, Pérez-Ríos J. Trap-Assisted Complexes in Cold Atom-Ion Collisions. Phys Rev Lett 2023; 130:143003. [PMID: 37084427 DOI: 10.1103/physrevlett.130.143003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 02/05/2023] [Accepted: 03/02/2023] [Indexed: 05/03/2023]
Abstract
We theoretically investigate the trap-assisted formation of complexes in atom-ion collisions and their impact on the stability of the trapped ion. The time-dependent potential of the Paul trap facilitates the formation of temporary complexes by reducing the energy of the atom, which gets temporarily stuck in the atom-ion potential. As a result, those complexes significantly impact termolecular reactions leading to molecular ion formation via three-body recombination. We find that complex formation is more pronounced in systems with heavy atoms, but the mass has no influence on the lifetime of the transient state. Instead, the complex formation rate strongly depends on the amplitude of the ion's micromotion. We also show that complex formation persists even in the case of a time-independent harmonic trap. In this case, we find higher formation rates and longer lifetimes than in Paul traps, indicating that the atom-ion complex plays an essential role in atom-ion mixtures in optical traps.
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Affiliation(s)
- H Hirzler
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XH Amsterdam, Netherlands
| | - E Trimby
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XH Amsterdam, Netherlands
| | - R Gerritsma
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XH Amsterdam, Netherlands
- QuSoft, Science Park 123, 1098 XG Amsterdam, Netherlands
| | - A Safavi-Naini
- QuSoft, Science Park 123, 1098 XG Amsterdam, Netherlands
- Institute for Theoretical Physics, Institute of Physics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - J Pérez-Ríos
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, USA
- Institute for Advanced Computational Science, Stony Brook University, Stony Brook, New York 11794, USA
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Hirzler H, Lous RS, Trimby E, Pérez-Ríos J, Safavi-Naini A, Gerritsma R. Observation of Chemical Reactions between a Trapped Ion and Ultracold Feshbach Dimers. Phys Rev Lett 2022; 128:103401. [PMID: 35333077 DOI: 10.1103/physrevlett.128.103401] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
We measure chemical reactions between a single trapped ^{174}Yb^{+} ion and ultracold Li_{2} dimers. This produces LiYb^{+} molecular ions that we detect via mass spectrometry. We explain the reaction rates by modeling the dimer density as a function of the magnetic field and obtain excellent agreement when we assume the reaction to follow the Langevin rate. Our results present a novel approach towards the creation of cold molecular ions and point to the exploration of ultracold chemistry in ion molecule collisions. What is more, with a detection sensitivity below molecule densities of 10^{14} m^{-3}, we provide a new method to detect low-density molecular gases.
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Affiliation(s)
- H Hirzler
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - R S Lous
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - E Trimby
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - J Pérez-Ríos
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin, Germany
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794, USA
| | - A Safavi-Naini
- QuSoft, Science Park 123, 1098 XG Amsterdam, The Netherlands
- Institute for Theoretical Physics, Institute of Physics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - R Gerritsma
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
- QuSoft, Science Park 123, 1098 XG Amsterdam, The Netherlands
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Ryan MD, Parkes AL, Corbett D, Dickie AP, Southey M, Andersen OA, Stein DB, Barbeau OR, Sanzone A, Thommes P, Barker J, Cain R, Compper C, Dejob M, Dorali A, Etheridge D, Evans S, Faulkner A, Gadouleau E, Gorman T, Haase D, Holbrow-Wilshaw M, Krulle T, Li X, Lumley C, Mertins B, Napier S, Odedra R, Papadopoulos K, Roumpelakis V, Spear K, Trimby E, Williams J, Zahn M, Keefe AD, Zhang Y, Soutter HT, Centrella PA, Clark MA, Cuozzo JW, Dumelin CE, Deng B, Hunt A, Sigel EA, Troast DM, DeJonge BLM. Discovery of Novel UDP- N-Acetylglucosamine Acyltransferase (LpxA) Inhibitors with Activity against Pseudomonas aeruginosa. J Med Chem 2021; 64:14377-14425. [PMID: 34569791 DOI: 10.1021/acs.jmedchem.1c00888] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This study describes a novel series of UDP-N-acetylglucosamine acyltransferase (LpxA) inhibitors that was identified through affinity-mediated selection from a DNA-encoded compound library. The original hit was a selective inhibitor of Pseudomonas aeruginosa LpxA with no activity against Escherichia coli LpxA. The biochemical potency of the series was optimized through an X-ray crystallography-supported medicinal chemistry program, resulting in compounds with nanomolar activity against P. aeruginosa LpxA (best half-maximal inhibitory concentration (IC50) <5 nM) and cellular activity against P. aeruginosa (best minimal inhibitory concentration (MIC) of 4 μg/mL). Lack of activity against E. coli was maintained (IC50 > 20 μM and MIC > 128 μg/mL). The mode of action of analogues was confirmed through genetic analyses. As expected, compounds were active against multidrug-resistant isolates. Further optimization of pharmacokinetics is needed before efficacy studies in mouse infection models can be attempted. To our knowledge, this is the first reported LpxA inhibitor series with selective activity against P. aeruginosa.
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Affiliation(s)
- M Dominic Ryan
- X-Biotix Therapeutics, 465 Waverly Oaks Road, Waltham, Massachusetts 02452, United States
| | - Alastair L Parkes
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - David Corbett
- Evotec UK, Anti-infectives, Block 23F, Alderley Park, Cheshire SK10 4TG, U.K
| | - Anthony P Dickie
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Michelle Southey
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Ole A Andersen
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Daniel B Stein
- Evotec SE, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | - Olivier R Barbeau
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Angelo Sanzone
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Pia Thommes
- Evotec UK, Anti-infectives, Block 23F, Alderley Park, Cheshire SK10 4TG, U.K
| | - John Barker
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Ricky Cain
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Christel Compper
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Magali Dejob
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Alain Dorali
- Evotec UK, Anti-infectives, Block 23F, Alderley Park, Cheshire SK10 4TG, U.K
| | - Donnya Etheridge
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Sian Evans
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Adele Faulkner
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Elise Gadouleau
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Timothy Gorman
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Denes Haase
- Evotec SE, Manfred Eigen Campus, Essener Bogen 7, 22419 Hamburg, Germany
| | | | - Thomas Krulle
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Xianfu Li
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Christopher Lumley
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Barbara Mertins
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Spencer Napier
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Rajesh Odedra
- Evotec UK, Anti-infectives, Block 23F, Alderley Park, Cheshire SK10 4TG, U.K
| | - Kostas Papadopoulos
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | | | - Kate Spear
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Emily Trimby
- Evotec UK, Anti-infectives, Block 23F, Alderley Park, Cheshire SK10 4TG, U.K
| | - Jennifer Williams
- Evotec UK, Anti-infectives, Block 23F, Alderley Park, Cheshire SK10 4TG, U.K
| | - Michael Zahn
- Evotec, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, U.K
| | - Anthony D Keefe
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Ying Zhang
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Holly T Soutter
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Paolo A Centrella
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Matthew A Clark
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - John W Cuozzo
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | | | - Boer Deng
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Avery Hunt
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Eric A Sigel
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Dawn M Troast
- X-Chem, 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Boudewijn L M DeJonge
- X-Biotix Therapeutics, 465 Waverly Oaks Road, Waltham, Massachusetts 02452, United States
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